Example usage for com.mongodb DBObject put

Introduction

In this page you can find the example usage for com.mongodb DBObject put.

Prototype

Object put(String key, Object v);

Source Link

Document

Sets a name/value pair in this object.

Usage

From source file:act.server.MongoDB.java

License:Open Source License

public void updateEstimatedEnergy(Reaction reaction) {
    BasicDBObject query = new BasicDBObject().append("_id", reaction.getUUID());
    DBObject obj = this.dbReactions.findOne(query);
    obj.put("estimateEnergy", reaction.getEstimatedEnergy());
    this.dbReactions.update(query, obj);
}

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From source file:act.server.MongoDB.java

License:Open Source License

public void updateReactionRefsOf(Seq seq) {
    BasicDBObject query = new BasicDBObject().append("_id", seq.getUUID());
    DBObject obj = this.dbSeq.findOne(query);
    BasicDBList refs = new BasicDBList();
    for (Long r : seq.getReactionsCatalyzed())
        refs.add(r);/*from   w w w  . ja va 2s .  c  om*/

    obj.put("rxn_refs", refs);
    this.dbSeq.update(query, obj);
}

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From source file:act.server.MongoDB.java

License:Open Source License

public void updateKeywordsCascade(Long id, Set<String> kwrds, Set<String> ciKwrds) {
    BasicDBObject query = new BasicDBObject().append("_id", id);
    DBObject obj = this.dbCascades.findOne(query);
    obj.put("keywords", kwrds);
    obj.put("keywords_case_insensitive", ciKwrds);
    this.dbCascades.update(query, obj);
}

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From source file:act.server.MongoDB.java

License:Open Source License

public void updateKeywordsWaterfall(Long id, Set<String> kwrds, Set<String> ciKwrds) {
    BasicDBObject query = new BasicDBObject().append("_id", id);
    DBObject obj = this.dbWaterfalls.findOne(query);
    obj.put("keywords", kwrds);
    obj.put("keywords_case_insensitive", ciKwrds);
    this.dbWaterfalls.update(query, obj);
}

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From source file:act.server.MongoDB.java

License:Open Source License

public void updateKeywords(Reaction reaction) {
    BasicDBObject query = new BasicDBObject().append("_id", reaction.getUUID());
    DBObject obj = this.dbReactions.findOne(query);
    obj.put("keywords", reaction.getKeywords());
    obj.put("keywords_case_insensitive", reaction.getCaseInsensitiveKeywords());
    this.dbReactions.update(query, obj);
}

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From source file:act.server.MongoDB.java

License:Open Source License

public void updateActReaction(Reaction r, int id) {
    // db.collection.update(query, update, options)
    // updates document(s) that match query with the update doc
    // Ref: http://docs.mongodb.org/manual/reference/method/db.collection.update/
    ////from  w ww  .  j a  va 2  s.  c  o m
    // Update doc: Can be { $set : { <field> : <val> } }
    // in case you need to keep the old document, but just update
    // some fields inside of it.
    // Ref: http://docs.mongodb.org/manual/reference/operator/update/set/
    //
    // But here (and in updateActChemical) we want to overwrite
    // the entire document with a new one, and so
    // a simple update call with the new document is what we need.

    BasicDBObject doc = createReactionDoc(r, id);
    DBObject query = new BasicDBObject();
    query.put("_id", id);
    this.dbReactions.update(query, doc);
}

---

From source file:act.server.MongoDB.java

License:Open Source License

public static BasicDBObject createReactionDoc(Reaction r, int id) {
    BasicDBObject doc = new BasicDBObject();
    doc.put("_id", id);
    doc.put("ecnum", r.getECNum());
    doc.put("easy_desc", r.getReactionName());

    BasicDBList substr = new BasicDBList();
    Long[] ss = r.getSubstrates();
    for (int i = 0; i < ss.length; i++) {
        DBObject o = getObject("pubchem", ss[i]);
        o.put("coefficient", r.getSubstrateCoefficient(ss[i]));
        substr.put(i, o);//from  w  w w .j a  v  a  2  s .c  o m
    }

    BasicDBList prods = new BasicDBList();
    Long[] pp = r.getProducts();
    for (int i = 0; i < pp.length; i++) {
        DBObject o = getObject("pubchem", pp[i]);
        o.put("coefficient", r.getProductCoefficient(pp[i]));
        prods.put(i, o);
    }

    BasicDBList prodCofactors = new BasicDBList();
    Long[] ppc = r.getProductCofactors();
    for (int i = 0; i < ppc.length; i++) {
        DBObject o = getObject("pubchem", ppc[i]);
        prodCofactors.put(i, o);
    }

    BasicDBList substrCofactors = new BasicDBList();
    Long[] ssc = r.getSubstrateCofactors();
    for (int i = 0; i < ssc.length; i++) {
        DBObject o = getObject("pubchem", ssc[i]);
        substrCofactors.put(i, o);
    }

    BasicDBList coenzymes = new BasicDBList();
    Long[] coenz = r.getCoenzymes();
    for (int i = 0; i < coenz.length; i++) {
        DBObject o = getObject("pubchem", coenz[i]);
        coenzymes.put(i, o);
    }

    BasicDBObject enz = new BasicDBObject();
    enz.put("products", prods);
    enz.put("substrates", substr);
    enz.put("product_cofactors", prodCofactors);
    enz.put("substrate_cofactors", substrCofactors);
    enz.put("coenzymes", coenzymes);
    doc.put("enz_summary", enz);

    doc.put("is_abstract", r.getRxnDetailType().name());

    if (r.getDataSource() != null)
        doc.put("datasource", r.getDataSource().name());

    if (r.getMechanisticValidatorResult() != null) {
        doc.put("mechanistic_validator_result", MongoDBToJSON.conv(r.getMechanisticValidatorResult()));
    }

    BasicDBList refs = new BasicDBList();
    for (P<Reaction.RefDataSource, String> ref : r.getReferences()) {
        BasicDBObject refEntry = new BasicDBObject();
        refEntry.put("src", ref.fst().toString());
        refEntry.put("val", ref.snd());
        refs.add(refEntry);
    }
    doc.put("references", refs);

    BasicDBList proteins = new BasicDBList();
    for (JSONObject proteinData : r.getProteinData()) {
        proteins.add(MongoDBToJSON.conv(proteinData));
    }
    doc.put("proteins", proteins);
    ConversionDirectionType cd = r.getConversionDirection();
    doc.put("conversion_direction", cd == null ? null : cd.toString());
    StepDirection psd = r.getPathwayStepDirection();
    doc.put("pathway_step_direction", psd == null ? null : psd.toString());

    return doc;
}

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From source file:act.server.MongoDB.java

License:Open Source License

public void submitToPubmedDB(PubmedEntry entry) {
    List<String> xPath = new ArrayList<String>();
    xPath.add("MedlineCitation");
    xPath.add("PMID");
    int pmid = Integer.parseInt(entry.getXPathString(xPath));
    if (this.dbPubmed != null) {
        WriteResult result;//w ww  . j  a v  a 2s .  co  m
        if (alreadyEntered(entry, pmid))
            return;
        DBObject doc = (DBObject) JSON.parse(entry.toJSON());
        doc.put("_id", pmid);
        this.dbPubmed.insert(doc);
    } else
        Logger.printf(0, "Pubmed Entry [%d]: %s\n", pmid, entry); // human readable...
}

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From source file:act.server.MongoDB.java

License:Open Source License

public List<Long> getRxnsWithSubstrate(String enzyme, Long org, List<Long> substrates) {
    BasicDBObject query = new BasicDBObject();
    query.put("organisms.id", org);
    BasicDBObject enzymeQuery = new BasicDBObject();
    enzymeQuery.put("ecnum", enzyme);
    query.put("$ne", enzymeQuery);
    for (Long substrate : substrates) {
        BasicDBList queryList = new BasicDBList();
        DBObject querySubstrate = new BasicDBObject();
        querySubstrate.put("enz_summary.substrates.pubchem", substrate);
        DBObject queryProduct = new BasicDBObject();
        queryProduct.put("enz_summary.products.pubchem", substrate);
        queryList.add(querySubstrate);//from  w  w  w . j  av a  2 s .  c  o  m
        queryList.add(queryProduct);
        query.put("$or", queryList);
    }

    DBCursor cur = this.dbReactions.find(query);
    List<Long> reactions = new ArrayList<Long>();
    while (cur.hasNext()) {
        DBObject o = cur.next();
        long id = (Integer) o.get("_id"); // checked: db type IS int
        reactions.add(id);
    }
    cur.close();
    return reactions;
}

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From source file:act.server.MongoDB.java

License:Open Source License

public long getChemicalIDFromName(String chemName, boolean caseInsensitive) {
    BasicDBObject query = new BasicDBObject();
    DBObject brenda = new BasicDBObject();
    DBObject pubchem = new BasicDBObject();
    DBObject synonyms = new BasicDBObject();
    if (caseInsensitive) {
        String escapedName = Pattern.quote(chemName);
        Pattern regex = Pattern.compile("^" + escapedName + "$", Pattern.CASE_INSENSITIVE);
        brenda.put("names.brenda", regex);
        pubchem.put("names.pubchem.values", regex);
        synonyms.put("names.synonyms", regex);
    } else {/*from  ww  w.  java2  s  .co m*/
        brenda.put("names.brenda", chemName);
        pubchem.put("names.pubchem.values", chemName);
        synonyms.put("names.synonyms", chemName);
    }
    BasicDBList ors = new BasicDBList();
    ors.add(brenda);
    ors.add(pubchem);
    ors.add(synonyms);
    query.put("$or", ors);
    Long id;
    DBObject o = this.dbChemicals.findOne(query);
    if (o != null)
        id = (Long) o.get("_id"); // checked: db type IS Long
    else
        id = -1L;
    return id;
}

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